Table S3: RNA gene annotation

rRNA gene

Name / Counts
18s_rRNA / 5
28s_rRNA / 6
8s_rRNA* / 67

*In the output of RNAmmer, eukaryotic 5S RNA is named as 8s_RNA.

tRNA genes

Type / Anticodon / Counts
Ala / AGC / 7
Ala / CGC / 4
Ala / TGC / 2
Arg / ACG / 4
Arg / CCG / 4
Arg / CCT / 2
Arg / TCG / 4
Arg / TCT / 4
Asn / ATT / 1
Asn / GTT / 10
Asp / GTC / 9
Cys / GCA / 2
Gln / CTG / 8
Gln / TTG / 2
Glu / CTC / 8
Glu / TTC / 8
Gly / CCC / 4
Gly / GCC / 8
Gly / TCC / 10
His / GTG / 6
Ile / AAT / 7
Ile / GAT / 2
Ile / TAT / 2
Leu / AAG / 6
Leu / CAA / 5
Leu / CAG / 5
Leu / TAA / 5
Lys / CTT / 10
Lys / TTT / 7
Met / CAT / 19
Phe / GAA / 6
Pro / AGG / 6
Pro / CGG / 3
Pro / TGG / 10
Ser / AGA / 6
Ser / CGA / 5
Ser / GCT / 5
Ser / TGA / 2
Thr / AGT / 11
Thr / CGT / 10
Thr / TGT / 5
Trp / CCA / 4
Tyr / GTA / 7
Val / AAC / 4
Val / CAC / 4
Val / TAC / 2
Pseudo / CGG / 1
Pseudo / TAA / 1
Pseudo / TAG / 1
Pseudo / TAT / 2
Pseudo / TGA / 1
Pseudo / TGT / 2

Top 75 RNA families

Name / Counts
tRNA / 239
SL1 / 185
5S_rRNA / 68
U5 / 51
U2 / 39
U1 / 38
ceN72-3_ceN74-2 / 38
MIR1023 / 37
MIR821 / 37
MIR408 / 36
Histone3 / 31
SL2 / 27
MIR2118 / 25
U4 / 22
mir-42 / 21
MIR530 / 17
SCARNA7 / 17
mir-548 / 15
MIR1027 / 14
K_chan_RES / 12
U3 / 12
tRNA-Sec / 12
ACEA_U3 / 11
MIR811 / 10
U6 / 9
ceN30 / 9
mir-202 / 9
mir-172 / 8
mir-281 / 7
mir-605 / 7
mir-609 / 7
MIR398 / 6
MIR807 / 6
PK-G12rRNA / 6
SSU_rRNA_archaea / 6
SSU_rRNA_bacteria / 6
SSU_rRNA_eukarya / 6
mir-153 / 6
mir-1803 / 6
mir-186 / 6
mir-232 / 6
mir-3179 / 6
mir-48 / 6
mir-576 / 6
mir-81 / 6
ceN28 / 5
mir-32 / 5
mir-449 / 5
MIR1444 / 4
MIR396 / 4
MIR397 / 4
SNORA73 / 4
SNORD14 / 4
SNORD15 / 4
ceN108 / 4
ceN109 / 4
ceN70 / 4
mir-1 / 4
mir-250 / 4
mir-788 / 4
sn3071 / 4
5_8S_rRNA / 3
RNase_MRP / 3
ceN89 / 3
mir-197 / 3
mir-231 / 3
mir-234 / 3
mir-255 / 3
mir-280 / 3
mir-367 / 3
mir-395 / 3
mir-399 / 3
mir-85 / 3
mir-942 / 3
mir-944 / 3

Table S4: Splice leader sequences found in EST libraries

Ce_SL1 / GGTTTAATTACCCAAGTTTGAG
Ce_SL2 / GGTTTTAACCCAGTTACTCAAG
Dc_SL2* / GGTTATTACCCAGTTACTCAAG

*new sequence

Table S5: List of transposon-like sequences

D. coronatus / C. elegans*
Number / Average length (bp) / Number / Average length (bp)
DNA transposons / 84 / 382 / 107 / 649
Helitron / 1 / 1743 / 5 / 891
LTR / 5 / 256 / 11 / 1403
Non-LTR / 14 / 683 / 23 / 707

* Data from C. elegans genome [89] for comparison.

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